So you're looking for a lost treasure ship on the bottom of the ocean. Good thing that the ocean is a perfect preservative. Oh, it might have some barnacles and coral here and there, maybe some parts have collapsed, but that may have happened when it was sunk. Heck, it probably still has tattered sails! It'll be sitting slightly to one side, but still mostly upright.

Not so in the real world. In the real world, water, particularly salt water, and especially warm salt water as seen in most pirate-frequented areas, wreaks havoc on anything immersed in it for too long. Just look at the continued decay of the Titanic or ships sunk during World War II. A wooden ship in salt water would be shipworm bait in no time flat.

Examples:

Anime

HIJMS Yamato, despite exploding, being blown into two pieces, and being thoroughly and definitively sunk by around twenty bomb and torpedo hits off Okinawa in 1945, remains in good enough condition to be converted into a space battleship centuries later.

In The Goonies, One-Eyed Willie's 350-year-old pirate ship actually sails out onto the open seas at the end. While the ship is not submerged, it has been sitting in water for three centuries in a wet, brackish cavern with lots of moisture dripping from stalactites. Aside from the skeleton of Willie, the ship and even its sails appear to be in fairly good condition.

Raise the Titanic! operates on the assumption that the ship was still in one piece, when Science Marches On and we now know it's in two very disparate fragments. While the ship sinking in one piece was the dominant theory at the time the film and its source novel were created, it's much harder to excuse how the ship is in nearly pristine condition, with all masts, rigging and even the glass skylight dome depicted as surviving perfectly intact after almost 70 years at the bottom of the Atlantic Ocean.

Literature

The ghost ships in Going Postal. They essentially work on the assumption that Water Is Air and the ships sink to a depth they can "float" at, instead of all the way to the bottom. However, they do eventually disintegrate.

In Final Fantasy X, the Al Bhed retrieve the Global Airship from the bottom of the sea, where it's been for a thousand years. And they get it working. The continued existence of lots of Machina a millenium after the production thereof was banned implies that the ancients reallybuilt to last.

Hostile Waters makes an effort to play this as straight as possible while also subverting it. Antaeus Cruiser 00 is in remarkably good condition after spending 20 years on the ocean bed. It manages to surface and set sailing just fine despite the long rest. Thankfully, nothing essential got damaged too badly, so after a visit in a dry dock the ship is at (or at least, near) full operational capacity, though they are signs she never gets as good as new. 00's sister ship, 04 isn't as lucky. She doesn't wake from her nap on the ocean bed. They justify this through the use of advanced nanotechnology. Both 00 and 04 have creation engines on board with trillions of the little things, which would have repaired 04, too, if it had received the signal.

In Dark Cloud, there is the Shipwreck. Despite having been sunk one hundred years prior, it looks like if it were lifted to the surface, had a certain large hole patched up, and given new sails, you could use it to sail the high seas.

Risk of Rain has a starship variation of this. You have to escape on the exact same spacecraft you crashed in. Which is not just a fighter but a massive freighter ship, cargo and all. And you're just one guy, possibly with no knowledge of ships or even technology at all. So unless they make them really hardy so as to survive a crash complete with cargo scattering, this trope is in full effect.

The Fallout 3 expansion Point Lookout has a Chinese spy sub that has to be entered to complete a side quest. The sub is still airtight after sinking over a century ago.

Part 2 of the DucktalesFive-Episode Pilot features a well-preserved shipwreck... in a desert that gets flooded by monsoon rains every hundred years or so, making it a bit more justified than normal. It's a bit less believable that it's in good enough condition to only need a bit of work before Scrooge and his nephews can attempt to sail it back home.

The Vasa, a fine example of royal idiocy, sank in the harbor in 1627. Said harbor is in the Baltic, an in-water sea that's brackish rather than seawater salty and is therefore free of the shipworm. The ship was salvaged in 1961 and is on display.

Thanks to mitigating factors including a shorter time frame and the cooler waters of the English Channel, a Sherman tank known to have fallen into the ocean during the D-Day invasion was salvaged for the 50th anniversary commemoration. It cleaned up nicely enough to fire live rounds. For "decades of seawater" levels of "cleanup."

The Dead Sea, on the other hand, is so salty that it preserves things due to the fact that very few things that would eat away at wrecks survive. A relatively recent expedition unearthed an ancient wooden ship in almost perfect condition.

The Great Lakes are fresh water so the wrecks of ships, even those of wooden sailing ships a couple of centuries old, are amazingly well-preserved.

The Black Sea has two distinctive layers. The deeper layer is very anoxic and nothing can live in it. Ancient ships that sunk near or under that layer—as well as signs of settlements from when the Sea was a freshwater lake—are found almost perfectly preserved.

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